[2023-06-13 05:35:21,246] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:35:21,248] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:35:21,248] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc4cf10c-b1d5-4e98-96a0-b1e62f6e780f/dqc_reference
[2023-06-13 05:35:22,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:35:22,596] [INFO] Task started: Prodigal
[2023-06-13 05:35:22,596] [INFO] Running command: gunzip -c /var/lib/cwl/stg688a1004-beb0-4488-8648-20cfd4bfb176/GCA_022767595.1_ASM2276759v1_genomic.fna.gz | prodigal -d GCA_022767595.1_ASM2276759v1_genomic.fna/cds.fna -a GCA_022767595.1_ASM2276759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:35:36,404] [INFO] Task succeeded: Prodigal
[2023-06-13 05:35:36,404] [INFO] Task started: HMMsearch
[2023-06-13 05:35:36,405] [INFO] Running command: hmmsearch --tblout GCA_022767595.1_ASM2276759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc4cf10c-b1d5-4e98-96a0-b1e62f6e780f/dqc_reference/reference_markers.hmm GCA_022767595.1_ASM2276759v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:35:36,658] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:35:36,660] [INFO] Found 6/6 markers.
[2023-06-13 05:35:36,686] [INFO] Query marker FASTA was written to GCA_022767595.1_ASM2276759v1_genomic.fna/markers.fasta
[2023-06-13 05:35:36,686] [INFO] Task started: Blastn
[2023-06-13 05:35:36,686] [INFO] Running command: blastn -query GCA_022767595.1_ASM2276759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc4cf10c-b1d5-4e98-96a0-b1e62f6e780f/dqc_reference/reference_markers.fasta -out GCA_022767595.1_ASM2276759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:35:37,307] [INFO] Task succeeded: Blastn
[2023-06-13 05:35:37,310] [INFO] Selected 20 target genomes.
[2023-06-13 05:35:37,310] [INFO] Target genome list was writen to GCA_022767595.1_ASM2276759v1_genomic.fna/target_genomes.txt
[2023-06-13 05:35:37,346] [INFO] Task started: fastANI
[2023-06-13 05:35:37,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg688a1004-beb0-4488-8648-20cfd4bfb176/GCA_022767595.1_ASM2276759v1_genomic.fna.gz --refList GCA_022767595.1_ASM2276759v1_genomic.fna/target_genomes.txt --output GCA_022767595.1_ASM2276759v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:35:51,045] [INFO] Task succeeded: fastANI
[2023-06-13 05:35:51,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc4cf10c-b1d5-4e98-96a0-b1e62f6e780f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:35:51,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc4cf10c-b1d5-4e98-96a0-b1e62f6e780f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:35:51,047] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:35:51,047] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 05:35:51,047] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-13 05:35:51,063] [INFO] DFAST Taxonomy check result was written to GCA_022767595.1_ASM2276759v1_genomic.fna/tc_result.tsv
[2023-06-13 05:35:51,064] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:35:51,064] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:35:51,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc4cf10c-b1d5-4e98-96a0-b1e62f6e780f/dqc_reference/checkm_data
[2023-06-13 05:35:51,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:35:51,096] [INFO] Task started: CheckM
[2023-06-13 05:35:51,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022767595.1_ASM2276759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022767595.1_ASM2276759v1_genomic.fna/checkm_input GCA_022767595.1_ASM2276759v1_genomic.fna/checkm_result
[2023-06-13 05:36:34,181] [INFO] Task succeeded: CheckM
[2023-06-13 05:36:34,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:36:34,205] [INFO] ===== Completeness check finished =====
[2023-06-13 05:36:34,205] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:36:34,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022767595.1_ASM2276759v1_genomic.fna/markers.fasta)
[2023-06-13 05:36:34,206] [INFO] Task started: Blastn
[2023-06-13 05:36:34,206] [INFO] Running command: blastn -query GCA_022767595.1_ASM2276759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc4cf10c-b1d5-4e98-96a0-b1e62f6e780f/dqc_reference/reference_markers_gtdb.fasta -out GCA_022767595.1_ASM2276759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:36:34,996] [INFO] Task succeeded: Blastn
[2023-06-13 05:36:35,001] [INFO] Selected 20 target genomes.
[2023-06-13 05:36:35,001] [INFO] Target genome list was writen to GCA_022767595.1_ASM2276759v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:36:35,019] [INFO] Task started: fastANI
[2023-06-13 05:36:35,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg688a1004-beb0-4488-8648-20cfd4bfb176/GCA_022767595.1_ASM2276759v1_genomic.fna.gz --refList GCA_022767595.1_ASM2276759v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022767595.1_ASM2276759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:36:44,145] [INFO] Task succeeded: fastANI
[2023-06-13 05:36:44,166] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 05:36:44,167] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_900316045.1	s__Cryptobacteroides sp900316045	98.1096	724	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.88	98.47	0.88	0.73	37	conclusive
GCA_002320605.1	s__Cryptobacteroides sp002320605	93.8489	700	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544195.1	s__Cryptobacteroides sp900544195	77.4492	109	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.99	97.97	0.92	0.84	3	-
GCA_000433355.1	s__Cryptobacteroides sp000433355	77.3864	121	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	97.93	0.86	0.80	6	-
GCA_902801885.1	s__Cryptobacteroides sp902801885	76.8938	88	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.96	97.31	0.90	0.87	8	-
GCA_002438845.1	s__Cryptobacteroides sp002438845	76.8583	117	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.65	99.58	0.89	0.89	3	-
GCA_902779765.1	s__Cryptobacteroides sp902779765	76.7229	84	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_902785825.1	s__Cryptobacteroides sp902785825	76.6347	79	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.93	95.98	0.90	0.88	3	-
GCA_004552965.1	s__Cryptobacteroides sp004552965	76.6341	83	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.55	98.04	0.91	0.85	9	-
GCA_902801205.1	s__Cryptobacteroides sp902801205	76.6095	68	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.36	98.05	0.90	0.89	3	-
GCA_018066065.1	s__Cryptobacteroides sp018066065	76.4205	57	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 05:36:44,169] [INFO] GTDB search result was written to GCA_022767595.1_ASM2276759v1_genomic.fna/result_gtdb.tsv
[2023-06-13 05:36:44,170] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:36:44,172] [INFO] DFAST_QC result json was written to GCA_022767595.1_ASM2276759v1_genomic.fna/dqc_result.json
[2023-06-13 05:36:44,173] [INFO] DFAST_QC completed!
[2023-06-13 05:36:44,173] [INFO] Total running time: 0h1m23s